.TH grompp 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
grompp - makes a run input file

.B VERSION 4.5
.SH SYNOPSIS
\f3grompp\fP
.BI "\-f" " grompp.mdp "
.BI "\-po" " mdout.mdp "
.BI "\-c" " conf.gro "
.BI "\-r" " conf.gro "
.BI "\-rb" " conf.gro "
.BI "\-n" " index.ndx "
.BI "\-p" " topol.top "
.BI "\-pp" " processed.top "
.BI "\-o" " topol.tpr "
.BI "\-t" " traj.trr "
.BI "\-e" " ener.edr "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-[no]v" ""
.BI "\-time" " real "
.BI "\-[no]rmvsbds" ""
.BI "\-maxwarn" " int "
.BI "\-[no]zero" ""
.BI "\-[no]renum" ""
.SH DESCRIPTION
\&The gromacs preprocessor
\&reads a molecular topology file, checks the validity of the
\&file, expands the topology from a molecular description to an atomic
\&description. The topology file contains information about
\&molecule types and the number of molecules, the preprocessor
\&copies each molecule as needed. 
\&There is no limitation on the number of molecule types. 
\&Bonds and bond\-angles can be converted into constraints, separately
\&for hydrogens and heavy atoms.
\&Then a coordinate file is read and velocities can be generated
\&from a Maxwellian distribution if requested.
\&grompp also reads parameters for the mdrun 
\&(eg. number of MD steps, time step, cut\-off), and others such as
\&NEMD parameters, which are corrected so that the net acceleration
\&is zero.
\&Eventually a binary file is produced that can serve as the sole input
\&file for the MD program.


\&grompp uses the atom names from the topology file. The atom names
\&in the coordinate file (option \fB \-c\fR) are only read to generate
\&warnings when they do not match the atom names in the topology.
\&Note that the atom names are irrelevant for the simulation as
\&only the atom types are used for generating interaction parameters.


\&grompp uses a built\-in preprocessor to resolve includes, macros 
\&etcetera. The preprocessor supports the following keywords:

\&ifdef VARIABLE

\&ifndef VARIABLE

\&else

\&endif

\&define VARIABLE

\&undef VARIABLE
include "filename"

\&include filename

\&The functioning of these statements in your topology may be modulated by
\&using the following two flags in your \fB mdp\fR file:

\&define = \-DVARIABLE1 \-DVARIABLE2

\&include = /home/john/doe

\&For further information a C\-programming textbook may help you out.
\&Specifying the \fB \-pp\fR flag will get the pre\-processed
\&topology file written out so that you can verify its contents.


\&If your system does not have a c\-preprocessor, you can still
\&use grompp, but you do not have access to the features 
\&from the cpp. Command line options to the c\-preprocessor can be given
\&in the \fB .mdp\fR file. See your local manual (man cpp).


\&When using position restraints a file with restraint coordinates
\&can be supplied with \fB \-r\fR, otherwise restraining will be done
\&with respect to the conformation from the \fB \-c\fR option.
\&For free energy calculation the the coordinates for the B topology
\&can be supplied with \fB \-rb\fR, otherwise they will be equal to
\&those of the A topology.


\&Starting coordinates can be read from trajectory with \fB \-t\fR.
\&The last frame with coordinates and velocities will be read,
\&unless the \fB \-time\fR option is used.
\&Note that these velocities will not be used when \fB gen_vel = yes\fR
\&in your \fB .mdp\fR file. An energy file can be supplied with
\&\fB \-e\fR to read Nose\-Hoover and/or Parrinello\-Rahman coupling
\&variables. Note that for continuation it is better and easier to supply
\&a checkpoint file directly to mdrun, since that always contains
\&the complete state of the system and you don't need to generate
\&a new run input file. Note that if you only want to change the number
\&of run steps tpbconv is more convenient than grompp.


\&Using the \fB \-morse\fR option grompp can convert the harmonic bonds
\&in your topology to morse potentials. This makes it possible to break
\&bonds. For this option to work you need an extra file in your $GMXLIB
\&with dissociation energy. Use the \-debug option to get more information
\&on the workings of this option (look for MORSE in the grompp.log file
\&using less or something like that).


\&By default all bonded interactions which have constant energy due to
\&virtual site constructions will be removed. If this constant energy is
\&not zero, this will result in a shift in the total energy. All bonded
\&interactions can be kept by turning off \fB \-rmvsbds\fR. Additionally,
\&all constraints for distances which will be constant anyway because
\&of virtual site constructions will be removed. If any constraints remain
\&which involve virtual sites, a fatal error will result.

To verify your run input file, please make notice of all warnings
\&on the screen, and correct where necessary. Do also look at the contents
\&of the \fB mdout.mdp\fR file, this contains comment lines, as well as
\&the input that \fB grompp\fR has read. If in doubt you can start grompp
\&with the \fB \-debug\fR option which will give you more information
\&in a file called grompp.log (along with real debug info). Finally, you
\&can see the contents of the run input file with the \fB gmxdump\fR
\&program.
.SH FILES
.BI "\-f" " grompp.mdp" 
.B Input, Opt.
 grompp input file with MD parameters 

.BI "\-po" " mdout.mdp" 
.B Output
 grompp input file with MD parameters 

.BI "\-c" " conf.gro" 
.B Input
 Structure file: gro g96 pdb tpr etc. 

.BI "\-r" " conf.gro" 
.B Input, Opt.
 Structure file: gro g96 pdb tpr etc. 

.BI "\-rb" " conf.gro" 
.B Input, Opt.
 Structure file: gro g96 pdb tpr etc. 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-p" " topol.top" 
.B Input
 Topology file 

.BI "\-pp" " processed.top" 
.B Output, Opt.
 Topology file 

.BI "\-o" " topol.tpr" 
.B Output
 Run input file: tpr tpb tpa 

.BI "\-t" " traj.trr" 
.B Input, Opt.
 Full precision trajectory: trr trj cpt 

.BI "\-e" " ener.edr" 
.B Input, Opt.
 Energy file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 0" 
 Set the nicelevel

.BI "\-[no]v"  "no    "
 Be loud and noisy

.BI "\-time"  " real" " \-1    " 
 Take frame at or first after this time.

.BI "\-[no]rmvsbds"  "yes   "
 Remove constant bonded interactions with virtual sites

.BI "\-maxwarn"  " int" " 0" 
 Number of allowed warnings during input processing

.BI "\-[no]zero"  "no    "
 Set parameters for bonded interactions without defaults to zero instead of generating an error

.BI "\-[no]renum"  "yes   "
 Renumber atomtypes and minimize number of atomtypes

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
